A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery

Tuesday, January 04, 2011

Oncogenesis Via Altered Enzyme Specificity, Part I

(Correction: a friend close to the story pointed out EZH2 is a lysine, not arginine methyltransferase. Stupid mistake! -- though I got it right once in the original version -- small consolation)

There's a bit of an involved story I've been meaning to put together & now another paper with a similar theme showed up. After some thought, I realized that the second story should go first.

Oncogenes are genes which when added to a cell can transform it to a cancerous state. A number of different classes of proteins can be oncogenic, but quite a few are either transcription factors or enzymes. I'm going to focus here on enzumes.

Oncogenic enzymes somehow have an enzymatic activity which promotes cell growth. A lot of oncogenic enzymes are protein kinases, and these can be activated by a number of mechanisms. For example, some are activating simply by being overexpressed, which in cancer occurs most commonly by amplification of the underlying chromosomal DNA. Another recurrent mechanism is the removal of inhibitory domains. Other changes alter the equilibrium between active and inactive states. Certain kinases are activated by dimerization, so some oncogenic mutations enhance dimerization. For example, in some fusion kinases, in which a chromosomal rearrangement has fused a kinase with another protein, a key role of the partner protein is to supply a dimerization motif.

The RAS family of GTPases are an interesting variant on this theme. RAS proteins (KRAS, HRAS and NRAS being the most important oncogenes) transmit growth-promoting signals when they have a bound GTP. They also have a slow GTPase activity which hydrolyzes the GTP to GDP, and when RAS proteins have GDP bound they no longer transmit the signal. Exchange of the GDP to GTP reactivates the growth signal. Oncogenic KRAS mutations slow or eliminate the GTPase activity; without this activity the gene never turns off. Hence, only a small number of possible mutations in KRAS will successfully turn it into an oncogene, since mutations must inactivate the GTPase without altering the other functions of the protein.

The two stories, one brand new related here and one which hit a fascinating milestone recently which will be in a future installment, are cases of additional ways enzymes can be altered to promote tumors. In each case, rather than activating or inactivating an enzyme the mutations succeed in tuning the activity of an enzyme in a way favorable to cancer.

Histone methyltransferases such as EZH2 add a methyl group to lysine residues (other methyltransferases can methylate arginine, which I mistaken pegged EZH2 in the original version of this). Any given lysine can actually have 4 different methylation states: none, single, double, or tri. This means in turn that an lysine methyltransferase has three types of substrates: those with 0, 1 or 2 existing methyl groups. What the new work shows is that Tyr641 is important in selecting the substrates, and these mutations focus the activity on converting dimethyl lysine to trimethyl lysine.

Several lines of evidence point to this conclusion. Two other lysine methyltransferases have been shown to prefer trimethylation when mutated in an analogous way. Molecular modeling suggests that this tyrosine serves to inhibit effective operation on dimethyl substrates. In vivo the mutation acts dominantly to increase trimethylated lysine levels on histones and in vitro the appropriate complex has an increased preference for dimethylated peptides.

This is the first such reported disease-causing mutation of this sort, though as noted above similar mutations have been created by scanning mutagenesis. Will we see other ones? There are many other homologous methyltransferases, but a quick sampling of COSMIC doesn't reveal a homolog with any recurrent pattern of mutation. It's worth keeping a lookout for one, but if not then a new mystery will remain to be explored: why is EZH2 special in this regard?

Going a bit farther afield, could there be oncogenic mutations in kinases which alter the substrate specificity? Given that some kinases require prior ("priming") phosphorylation of substrates, could a mutation in the kinase reduce this requirement? Alternatively, do some kinases phosphorylate both cancer-promoting and cancer-retarding substrates? If so, could mutations exist which shift the balance towards cancer promotion? Seems like a long shot, but who would have guessed in advance of mutations like the EZH2 ones?

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About Me

Dr. Robison spent 10 years at Millennium Pharmaceuticals working with various genomics & proteomics technologies & working on multiple teams attempting to apply these throughout the drug discovery process. He spent 2 years at Codon Devices working on a variety of protein & metabolic engineering projects as well as monitoring a high-throughput gene synthesis facility. After a brief bit of consulting, he rejoined the cancer drug discovery field at Infinity Pharmaceuticals in May 2009. In September 2011 he joined Warp Drive Bio, a startup applying genomics to natural product drug discovery. Other recurring characters in this blog are his loyal Shih Tzu Amanda and his teenaged son alias TNG (The Next Generation).
Dr. Robison can be reached via his Gmail account, keith.e.robison@gmail.com
You can also follow him on Twitter as @OmicsOmicsBlog.